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/*===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's official duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government have not placed any restriction on its use or reproduction.
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
*/
/*****************************************************************************
* GATB : Genome Assembly Tool Box
* Copyright (C) 2014 INRIA
* Authors: R.Chikhi, G.Rizk, E.Drezen
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as
* published by the Free Software Foundation, either version 3 of the
* License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*****************************************************************************/
/** \file LargeInt<2>.hpp
* \date 01/03/2013
* \author edrezen
* \brief Integer class relying on native u_int64_t type
*/
/********************************************************************************/
#if INT128_FOUND == 1
/********************************************************************************/
u_int64_t revcomp64 (const u_int64_t& x, size_t sizeKmer)
{
u_int64_t res = x;
unsigned char* kmerrev = (unsigned char *) (&(res));
unsigned char* kmer = (unsigned char *) (&(x));
for (size_t i=0; i<8; ++i) { kmerrev[8-1-i] = revcomp_4NT [kmer[i]]; }
return (res >> (2*( 32 - sizeKmer))) ;
}
template<> class LargeInt<2>
{
public:
/** Constructor.
* \param[in] c : initial value of the large integer. */
LargeInt<2>(const __uint128_t& c=0) noexcept { value[0] = c; }
LargeInt<2>(const std::string& kmer) noexcept : LargeInt<2>(0) {
int sizeKmer = kmer.size();
for (int i = 0; i < sizeKmer; i++) {
operator<<=(2);
value[0] += std::find(bin2NT.begin(), bin2NT.end(), kmer[i]) - bin2NT.begin();
}
}
template <typename T>
LargeInt<2>(const T& a, const T& b) noexcept : LargeInt<2>(0) {
for(T i = a; i < b; ++i) {
operator<<=(2);
value[0] += std::find(bin2NT.begin(), bin2NT.end(), *i) - bin2NT.begin();
}
}
u_int64_t getVal () const { return *value; }
static const char* getName () { return "LargeInt<2>"; }
static const size_t getSize () { return 8*sizeof(__uint128_t); }
LargeInt<2> operator+ (const LargeInt<2>& other) const { return value[0] + other.value[0]; }
LargeInt<2> operator- (const LargeInt<2>& other) const { return value[0] - other.value[0]; }
LargeInt<2> operator| (const LargeInt<2>& other) const { return value[0] | other.value[0]; }
LargeInt<2> operator* (const int& coeff) const { return value[0] * coeff; }
LargeInt<2> operator/ (const u_int32_t& divisor) const { return value[0] / divisor; }
u_int32_t operator% (const u_int32_t& divisor) const { return value[0] % divisor; }
LargeInt<2> operator^ (const LargeInt<2>& other) const { return value[0] ^ other.value[0]; }
LargeInt<2> operator& (const LargeInt<2>& other) const { return value[0] & other.value[0]; }
LargeInt<2> operator& (const char& other) const { return value[0] & other; }
LargeInt<2> operator~ () const { return ~value[0]; }
LargeInt<2> operator<< (const int& coeff) const { return value[0] << coeff; }
LargeInt<2> operator>> (const int& coeff) const { return value[0] >> coeff; }
bool operator!= (const LargeInt<2>& c) const { return value[0] != c.value[0]; }
bool operator== (const LargeInt<2>& c) const { return value[0] == c.value[0]; }
bool operator< (const LargeInt<2>& c) const { return value[0] < c.value[0]; }
bool operator<= (const LargeInt<2>& c) const { return value[0] <= c.value[0]; }
LargeInt<2>& operator+= (const LargeInt<2>& other) { value[0] += other.value[0]; return *this; }
LargeInt<2>& operator^= (const LargeInt<2>& other) { value[0] ^= other.value[0]; return *this; }
LargeInt<2>& operator<<= (const int& coeff) { value[0] <<= coeff; return *this; }
LargeInt<2>& operator>>= (const int& coeff) { value[0] >>= coeff; return *this; }
u_int8_t operator[] (size_t idx) const { return (value[0] >> (2*idx)) & 3; }
/** Output stream overload. NOTE: for easier process, dump the value in hexadecimal.
* \param[in] os : the output stream
* \param[in] in : the integer value to be output.
* \return the output stream.
*/
friend std::ostream & operator<<(std::ostream & os, const LargeInt<2> & in)
{
__uint128_t x = in.value[0];
u_int64_t high_nucl = (u_int64_t) (x>>64);
u_int64_t low_nucl = (u_int64_t)(x&((((__uint128_t)1)<<64)-1));
if (high_nucl == 0) { os << std::hex << low_nucl << std::dec; }
else { os << std::hex << high_nucl << "." << low_nucl << std::dec; }
return os;
}
/********************************************************************************/
/** Print corresponding kmer in ASCII
* \param[in] sizeKmer : kmer size (def=32).
*/
std::string toString (size_t sizeKmer) const
{
std::string seq(sizeKmer,'A');
for (size_t i=0; i<sizeKmer; i++) { seq[sizeKmer-i-1] = bin2NT [(*this)[i]]; }
return seq;
}
u_int64_t oahash() const {
return oahash64((u_int64_t)(value[0]>>64)) ^ oahash64 ((u_int64_t)(value[0]&((((__uint128_t)1)<<64)-1)));
}
/********************************************************************************/
template<typename Map>
static LargeInt<2> polynom (const char* data, size_t size, Map fct)
{
LargeInt<2> res (0);
for (size_t i=0; i<size; ++i) { res.value[0] = res.value[0] * 4 + fct(data[i]); }
return res;
}
u_int64_t* getPointer() { return reinterpret_cast<u_int64_t*>(value); }
const u_int64_t* getPointer() const { return reinterpret_cast<const u_int64_t*>(value); }
private:
friend LargeInt<2> revcomp (const LargeInt<2>& i, size_t sizeKmer);
__uint128_t value[1];
};
/********************************************************************************/
inline LargeInt<2> revcomp (const LargeInt<2>& in, size_t sizeKmer)
{
// ---64bits-- ---64bits--
// original kmer: [__high_nucl__|__low_nucl___]
//
// ex: [ AC | .......TG ]
//
//revcomp: [ CA | .......GT ]
// \_low_nucl__/\high_nucl/
const __uint128_t& x = in.value[0];
u_int64_t high_nucl = (u_int64_t)(x>>64);
int nb_high_nucl = sizeKmer>32?sizeKmer - 32:0;
__uint128_t revcomp_high_nucl = revcomp64 (high_nucl, nb_high_nucl);
if (sizeKmer<=32) revcomp_high_nucl = 0; // srsly dunno why this is needed. gcc bug? u_int64_t x ---> (x>>64) != 0
u_int64_t low_nucl = (u_int64_t)(x&((((__uint128_t)1)<<64)-1));
int nb_low_nucl = sizeKmer>32?32:sizeKmer;
__uint128_t revcomp_low_nucl = revcomp64 (low_nucl, nb_low_nucl);
return (revcomp_low_nucl<<(2*nb_high_nucl)) + revcomp_high_nucl;
}
/********************************************************************************/
#endif //INT128_FOUND
/********************************************************************************/
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